Some time before the Black Mesa Incident, scientists of the Black Mesa Research Facility discover the alien borderworld of Xen while developing teleportation technology.[4] Science expeditions performed by "Survey Teams" are secretly launched to study and collect data from Xen, using a huge teleport deep within the top-secret Sector F.[4] Despite the deaths of dozens of researchers, Xen inhabitants and wildlife are brought back to Earth for study in the Sector E.[5][6] Soon, members of the Xen Survey Teams recover several Xen crystals from the borderworld, which are to be studied in Sector C's Anti-Mass Spectrometer.

On May 11, 200-, L.M. writes a memo to Colette Green, with C.C. to Isaac Kleiner. In it, L.M. tells Green that the supervision team is particularly interested in Xen crystal sample GG-3883. Although Green's experiments on the sample revealed unexpected spectral analysis fluctuations, she has identified it as the purest and largest sample they have. Therefore sample GG-3883 replaces the original chosen sample, sample EP-0021, in the simulation. L.M. also states that the enclosed materials requisition form required to switch the samples has already been authorized, and is conscious that a sample change made so fast is a violation of normal anomalous material handling protocol.[7] These instructions likely come directly from Black Mesa Administrator Wallace Breen, who is known to have given specific instructions on that matter and is apparently keen on gaining conclusive results, added to behind the scenes influence by the G-Man, who apparently personally brought GG-3883 to Sector C.[8][9]

On May 16, 200-, the majority of Sector C is in full preparation for the experiment, but is delayed by Dr. Gordon Freeman, who is running late for his job in manually operating the Anti-Mass Spectrometer in Test Lab C-33/a.[10] This delay is actually convenient for the science team, who use the time for more preparations, and to recover from a minor system crash across the facility.[8] The Sector C staff also decide to boost the Anti-Mass Spectrometer to 105% power, much higher than the equipment's safety buffer zone of below 90%, in a bid to garner better data.[11]Eli Vance, one of the research leaders, argues against this decision but is overruled.[9]

Another scientist, Harold, warns his close friend Rosenberg about the danger of such an energy boost. Just before the experiment, Rosenberg discusses the matter with fellow scientist Richard Keller, but Keller states he has no power to change the operating levels because Breen insisted that the Anti-Mass Spectrometer run at the levels he set for it.[11] Because of this immense power output, Black Mesa experiences several minor blackouts.[12]

The Resonance Cascade causing destruction and teleports Vortigaunts into the test chamber.

As Dr. Freeman enters the test chamber, now donning his HEV Suit, Dr. Gina Crossdelivers the Xen crystal sample to the chamber while Dr. Colette Green works the Anti-Mass Spectrometer from its lower maintenance level.[11] It is also at this point that Eli Vance is contacted by the G-Man, who whispers to "prepare for unforeseen consequences". Vance contemplates aborting the test, but ultimately decides against it.[9] Freeman activates the device without incident, with the rest of the science team monitoring the experiment from the upper control room. As the Anti-Mass Spectrometer is boosted to full 105% capacity, one of the overseeing scientists notices a small discrepancy in the readings, but dismisses it as it goes back to acceptable bounds. The sample arrives at the test chamber, and Freeman pushes the Materials Handler holding the crystal into the beam of the Anti-Mass Spectrometer. The immediate result is catastrophic; the main beam of the device begins to violently pulsate and expand. The Anti-Mass Spectrometer explodes in several sections, and the science team scramble to shut it down, to no avail, and are killed by a violent beam of energy that cascades through the control room window. The Anti-Mass Spectrometer continues to go critical, and a Resonance Cascade occurs, ripping a hole through dimensional space and teleporting Xen creatures into the facility. The Resonance Cascade teleports Freeman to various locations around Xen, and after teleporting back into the test chamber, he slips into unconsciousness.[8]

The Resonance Cascade has immediate and catastrophic effects. The Xen creatures, trapped in an alien environment, begin to relentlessly attack Black Mesa employees on sight. The Resonance Cascade also causes serious structural damage to the facility, with elevators collapsing and ceilings caving in.[12][13] Freeman awakes in the test chamber an undetermined amount of time after the Cascade, with the Anti-Mass Spectrometer in pieces and sirens blaring throughout the ruined facility. As Gordon makes his way through what remains of Sector C, he discovers that some of the personnel survived the experiment, including Eli Vance, who Gordon finds treating a wounded scientist. Vance tells Gordon that all the phones in the facility have been knocked out, and sends Gordon towards the surface to get help.[13] Three of the survivors of the initial disaster, Dr. Gina Cross, Dr. Colette Green and Dr. Rosenberg, make their way to the surface and call in the military to help them with the alien onslaught. The military, in the form of the Hazardous Environment Combat Unit, arrive quickly, deploying troops, ordnance and vehicles via aircraft and trains.[14] Aside from dispatching the aliens, these troops are also instructed to permanently silence the facility personnel.[15]

A dead scientist in the alien-infested Sector D Office Complex.

The HECU's foray into the facility is initially successful. They manage to establish control of Black Mesa's surface facilities and began to make inroads into its extensive underground facilities, setting up several fortified outposts to keep the aliens at bay.[15] They also manage to capture Dr. Rosenberg, who sent the distress signal,[14] and lock him in a railway cargo car for interrogation.[16] Meanwhile, Barney Calhoun, a low-ranking security guard and personal friend of Freeman's, awakens in an elevator that collapsed moments following the Resonance Cascade.[17] Determined to escape the crumbling facility, he locates and frees Dr. Rosenberg. With his aid, Rosenberg reaches the old, abandoned A-17 Prototype Test Labs used for teleportation experiments. There, he hopes to use an old teleport to escape from the facility.[16] Calhoun helps the doctor first by traveling to Xen and activating a device necessary for successful teleportation, and then by finding and recharging a spare battery for the teleport.[18][19]

As Freeman makes his way towards the surface, he is told by surviving personnel that the military have arrived on the surface to rescue them.[20] Gordon passes through the alien-infested Sector DAdministration Center, and he finally reaches the Sector D High Security Storage Facility, where the HECU have established a large presence. Shortly after arrival however, Freeman witnesses a HECU marine murdering a scientist calling for help, revealing to him and the rest of the surviving employees the true nature of the HECU's presence. Freeman fights his way through the military encampment and takes a service elevator to the surface, only to find that minor air strikes have begun across the facility, and is forced to retreat back inside.[15]

While HECU establish their presence in the underground, Dr. Green and Dr. Cross, under the instruction of Dr. Keller, attempt to reactivate the damping locks to close the rift, but an alien force keeps it open. They then work to prepare the satellite delivery rocket for launch, which is essential for the work of the prototype displacement beacon, a device capable of reducing the effects of the Resonance Cascade. Cross and Green first find a living security guard who knows the all-clear codes needed to lift the military air-traffic lockdown. The two doctors then enter these codes, successfully lifting the lockdown and allowing the rocket to be launched. However, the launch is aborted when soldiers captured the control room and massacre its personnel.[21]

Calhoun then narrowly escapes through the portal with Rosenberg and his two colleagues, Walter Bennet and Simmons, just as the HECU soldiers storm the underground facility. While the doctors successfully reach the safe area outside of the Black Mesa, Calhoun is caught in a temporal harmonic reflux, traveling between Xen and the facility. However, he soon ends up together with the scientists and the four escape in an SUV.[22]

As the battle continues on the surface, Freeman is forced back into the depths of the facility, where he is told that the scientists of the Lambda Complex should be able to reverse the effects of the Resonance Cascade.[15] As the Black Mesa Transit System is down, Freeman sets out across the facility on foot, fighting his way to the rocket propulsion test chamber of Sector D, where a large Tentacle has been teleported. Freeman silently works his way around the creature and activates the oxygen, fuel and power necessary to activate the test rocket, then makes his way back to the chamber control room and test-fires it, killing the Tentacle nestled in the chamber.[23] Meanwhile, the HECU identify Freeman as the scientist indirectly responsible for the Resonance Cascade, and mark him as their number one target, using the tracking devices in his HEV Suit to locate him and set traps and ambushes.[24][25]

The HECU set up heavy turret emplacements to stop Freeman, and write graffiti to intimidate him.

Freeman makes his way into the Sector E Materials Transport, where HECU marines clash with a Gargantua on the main track turntable. The Gargantua quickly gains the upper hand and kills the marines. Freeman is told by a dying security guard in the track control room that if he restores power to the main generator he can ride the monorail to the surface. Freeman enters the Houndeye-infested subterranean areas and activates the generator, restoring power to the vicinity. Afterward, he is forced to kill the Gargantua to be able to board the monorail it guards.[26] As Freeman rides the rail car, he is told by a security guard that he must travel to the High Altitude Launch Center to launch a rocket, which Green, Cross, Keller and the Lambda Team can connect to a satellite and reverse the effects of the Resonance Cascade. Freeman is continuously hindered by the HECU on his way to the surface, who are intent to kill or capture him, setting up Laser Trip Mines, heavy turrets and rocket emplacements, and even attempt to intimidate Freeman through threatening, albeit misspelled, graffiti messages. Despite overwhelming odds, Freeman fights his way through all of these obstacles and reaches the Launch Center on the surface, by which time night has fallen. Upon clearing the Launch Center of marines, Freeman launches the rocket prepared by Doctors Green, Cross and Keller.[24] Afterward, Dr. Cross and Dr. Green, with the assistance of Dr. Keller, manually raise, power and activate the displacement beacon for the prototype equipment, thus initiating a resonance reversal to help lessen the effects of the dimensional rift, although not aborting it permanently. During the beacon's activation, both Green and Cross are caught in a harmonic reflux, but survive and return to Black Mesa.[27]

A Vortigaunt attacking Gordon in the run-down areas of Sector E.

Shortly after this, in response to the HECU's failing cleanup operation, the US government deploys a Black Ops strike team into Black Mesa to plant and detonate a Mark IV Thermonuclear Device to decimate the entire facility, intending to end the conflict once and for all, with orders to kill anything, human or otherwise, that stand in their way.[28] After the Black Ops' arrival, two Vortigaunts, X-8973 and R-4913, are successful in retrieving several stolen Xen crystals.[29] After Freeman journeys through the abandoned areas of Sector E, killing an Ichthyosaur, and coming in contact with members of the Black Ops, he is ambushed and knocked unconscious by two HECU marines. Instead of taking him for interrogation as ordered however, Freeman is stripped of his weapons and dumped by the two marines into a trash compactor, an event witnessed by Calhoun while caught in a harmonic reflux.[25] He narrowly escapes death and manages to work his way through Black Mesa's Biological Waste Processing Plant.[30] Upon exiting the plant, and restocking on some weapons, Freeman finds himself in Black Mesa's top-secret Alien Research Labs, where Xen creatures have been contained for study and examination, long before the incident even took place. Within, the HECU have established a considerable presence, but are clashing with hordes of escaped and teleported Xen hostiles. Freeman fights his way through the carnage, obtaining an experimental Tau Cannon in the process, and escorts a hiding scientist to open the main doors for him.[31] Freeman exits the lab and begins his journey across the surface.[32] Meanwhile, Corporal Adrian Shephard awakes in the Black Mesa Medical Lab, after being knocked unconscious following his Osprey Heliplane being shot down by Xen aircraft.[33] Shephard makes his way towards the extraction point, where he is told via radio that the military forces are pulling out of the facility.[34]

View of the canyon from the cliff side, where a HECU soldier waits for Freeman.

At this point, the surface has become a warzone. HECU forces clash with increasingly large numbers of Xen creatures, and require the assistance of M1A1 Abrams' and M2A3 Bradleys, with AH-64 Apaches patrolling the skies.[32] Even these heavy vehicles are not enough, and the tide of the battle begins to turn in favor of the aliens. Freeman makes his way across the surface as hostilities increase, traversing the Sector G dam, and slowly moves through the rocky Black Mesa desert while under fire from an overhead Apache. Freeman descends into the drainage systems and steps out onto a huge military-occupied cliff face overlooking an expansive desert canyon and the nearby river. Soldiers and Sentry Guns guard the cliff side, and after Freeman fights through them and retrieves a RPG on the far side of the cliff, another Apache appears. After a brief confrontation, Freeman destroys the Apache and moves back towards the facility to reach his goal - the Lambda Complex.[32]

At this point, the HECU determine that they are fighting a losing battle against the Xen aliens and, having continually failed to neutralize Freeman, abandon their mission and begin to evacuate the facility, calling in air strikes and heavy artillery to cover their retreat.[35] The Xen aliens do not relent however, and continue to attack en masse, killing any HECU troops that have not yet evacuated. Freeman is forced to traverse the carnage, and moves through the bombed-out buildings of the Topside Motorpool.[35] Meanwhile, Corporal Shephard and a squad of surviving marines prepare to terminate their hunt for Freeman and evacuate Black Mesa in an Osprey Heliplane. Shephard however, lagging behind, is locked out of the courtyard housing the Osprey by The G-Man. With no time left to spare and no way to open the door, the other marines are forced to leave without Shephard, unaware that The G-Man had even been present.[36] Shephard continues to journey through Black Mesa in search of both his comrades and an alternative escape route after being abandoned at the extraction point. After traveling through a zombie-infested blast furnace, Shephard meets several other marines from his company who have also been left behind. He joins forces with them as they try to escape from the facility.[37]

Gordon Freeman jumping into the Lambda Complex teleport.

Freeman meanwhile, makes his way into an underground storage garage to avoid the bombardments, and eventually fights his way through scores of aliens and several groups of the decimated HECU forces before reaching the Lambda Complex, where he has been told the science team are sheltering from the Xenians.[35] However, he finds that the majority of the complex is now overrun by hostile creatures. He is informed by a scientist that stayed behind that he must flood the reactor chambers in order to access the core, and that a team of scientists is waiting for him at the tip of the reactor.[4] Gordon navigates through the Lambda Core, facing numerous assaults from the Xen forces. After much struggle, Gordon finally reaches the inner laboratories of the complex, where the Lambda Team have been sheltering. Here he discovers that the Lambda Complex is where they developed the teleportation technology that allowed scientists to travel to Xen in the first place. The handful of surviving personnel, who have held themselves up in a small stronghold, inform Gordon that, unfortunately, the satellite he launched was not able to reverse the effects of the Resonance Cascade because an immensely powerful being on the other side is keeping the portal between the worlds open, and that Gordon must kill it to prevent the Xen aliens from taking over completely. Before being teleported to Xen, Gordon gains access to several ammunition, health and HEV-charge caches as well as the experimental Gluon Gun, and is finally reunited with the Long Jump Module. After an attempted intervention by Alien Controllers, the scientists activate the teleport and Gordon is teleported to Xen.[4]

Simultaneously, Shephard enters the chamber just in time to see Freeman disappearing into the portal. The Alien Controllers continue to attack, severely damaging the teleport and killing the controlling scientist in the process. Shephard is caught up in the carnage, and stumbles into a small portal discharged by the teleport, where he is transported into Xen. Shephard makes a short journey through Xen, and sees a scientist being teleported from a fatal height, holding the device that got him there - the Displacer Cannon. Shephard uses the device to teleport himself around several areas of Xen and Black Mesa before eventually ending up in Sector E.[38]

Freeman arrives at Xen after his teleportation at the Lambda Complex, and is almost immediately contacted telepathically by the Nihilanth, the creature holding the portal open, who responds to Freeman's arrival with "comes... another...". Freeman uses his Long Jump Module to traverse the floating islands of Xen, encountering many of the aliens that had been teleported into Black Mesa in their natural habitats, as well as the remains of HEV-wearing researchers that came before him. Freeman arrives at a large central island, and within finds a small portal, which he steps into and is teleported to the Gonarch's lair.[5]

Race X and Black Ops forces clash on the surface.

As the Black Ops assess the situation through interrogation of captured HECU soldiers, a new and unknown foe appears through the dimensional tear, the so-called Race X.[39] This new foe begins to attack anything left in the facility, including Xen creatures, hoping to clear the way for the Gene Worm, a massive Race X creature, to enter Earth and terraform it for Race X.[40] Meanwhile, Corporal Shephard travels between various biosphere chambers and laboratories featuring massive terrariums used to house Xen fauna being studied by the scientists deep within the Sector E Biodome Complex. While in Sector E, Shephard comes in contact with some of the newly arrived Race X creatures. Eventually he reaches Waste Processing Area 3, and picks up a radio transmission from a group of marines fighting a Pit Worm that has been teleported into a toxic waste chamber.[39] By the time Shephard arrives, the marines have been killed, and he is forced to kill the Pit Worm himself, dumping toxic waste onto the creature, and proceeds to make his way to the surface.[41] By the time Shephard reaches the surface, it has once again become a battlefield, with a fierce battle raging between the Race X creatures, the Black Ops contingent, including several snipers, and the remnants of the HECU. Shephard makes his way through the underground canals and sewers of Black Mesa, fighting through a Voltigore nest, and arrives at the Sector G hydroelectric dam. Here, a Gargantua has been trapped on top of the dam and several marines are attempting to kill it. Shephard uses explosives to destroy the creature and leaves the area through the dam's exposed water pipes.[42]

The Nihilanth battles with Freeman on Xen.

Meanwhile, Freeman battles and defeats the Gonarch and her Headcrab minions.[43] Gordon continues his journey across Xen, with supplies running short, wasted on destroying the Gonarch. Freeman traverses an expansive series of Xen islands, coming in contact with many Xen hostiles, and eventually finds himself in an Alien Grunt cloning facility. Within the factory, enslaved Vortigaunts are forced to work, but do not attack Freeman, perhaps to subtly rebel against their masters. After much fighting, and interception from Alien Grunts and Controllers, Freeman comes across a large, ominous portal on a lone series of floating islands.[44] Upon entering the portal, Freeman is faced with the Nihilanth; the holder of the interdimensional rift, the one responsible for the enslavement of the Vortigaunts, and leader of Xen forces.[45]

The G-Man reactivating the bomb.

Back at Black Mesa, Shephard discovers the mysterious Black Ops' plan for Black Mesa. Shephard finds a group of Black Ops in an underground parking garage under the Ordinance Storage Facility arming the Mark IV Thermonuclear Device that will destroy the facility once and for all. Shephard defeats the assassins, and deactivates the device. However, shortly afterward in a nearby room with a view of the warhead, Shephard witnesses The G-Man reactivating it, and he cannot go back to the bomb, as the path has been sealed making the destruction of Black Mesa inevitable.[46] After making his way through warehouses filled with Race X creatures and Black Ops fighting, Adrian Shephard arrives at an old industrial area of Black Mesa where the enormous Gene Worm is attempting to come through a portal from the Race X homeworld. Shephard uses mounted laser weapons to blind and kill it; in its death throes, an enormous teleportation portal spreads outwards and envelops him.[40] Shephard regains consciousness inside an Osprey Heliplane, confronted by the mysterious G-Man. As the G-Man talks to Shephard, the nuclear warhead detonates and Black Mesa is decimated in the distance. The G-Man then informs Shephard that he will be detained "in a place where you can do no possible harm, and where no harm can come to you." He explains this is done because Shephard reminds him of himself, but is still a dangerous witness. The G-Man walks into a portal, and Shephard is detained in a void of nothingness.[47]

The G-Man addresses Freeman on Xen.

On Xen, Freeman engages the Nihilanth in its lair. As Freeman battles the creature, it teleports him to several sub-caverns filled with Xen creatures. Freeman continuously escapes these caverns, and destroys the Nihilanth's shield, allowing him to destroy its vulnerable brain. As the creature dies, it floats toward the ceiling, and explodes in a giant green blast that overpowers Gordon's senses.[45] When he comes to, he is confronted by the G-Man. Both are transported to various locales around Xen, while the G-Man praises Gordon's actions in the borderworld. He explains that his "employers", agreeing that Gordon has "limitless potential", have authorized him to offer Freeman a job. The final teleportation takes Gordon to the same tramcar that he rode in on the morning of May 16, but apparently flying through space at immense speed. Gordon accepts this offer by stepping though a portal, and, finding himself floating in nothingness, hears the G-Man's voice one last time: "Wisely done, Mr. Freeman, I will see you up ahead...".[48]

The consequences of the Black Mesa Incident are massive. The relatively small inter-dimensional rift causes Portal Storms to rage across Earth, bringing large amounts of Xen wildlife to the planet. Earth governments set up protection centers across the planet as they try to deal with the hostile aliens. The continuing portal storms and dimensional fluctuations attract the attention of the Combine, an immense inter-dimensional empire that was responsible for chasing the Nihilanth and its minions to Xen in the first place. The Combine mount a full-scale invasion on Earth, prompting the United Nations to declare war on the Combine. The war ended when Combine completely overwhelm Earth military forces and smash opposition in a mere seven hours. The Combine hold position over the damaged United Nations headquarters in New York City where former-Black Mesa administrator Wallace Breen negotiated Earth's surrender saving the remnants of humanity at the expense of their freedom. Breen is appointed as Earth administrator, but is simply a puppet for the true rulers - the Combine Advisors.[49] The death of the Nihilanth also ends the slavery of the Vortigaunt race, earning Gordon Freeman their eternal gratitude.[50] Dr. Eli Vance convinces the Vortigaunts to side with humanity against the Combine, and the two species form an underground resistance aiming to overthrow their alien oppressors.[50]

Although the incident is largely considered to be a terrible accident, there is incidental evidence which suggests it is to some extent engineered. The Nihilanth seems to have been planning the invasion from Xen for some time,[45] and the G-Man more than once hints at his own manipulations of the affair, most notably when he whispers to Eli Vance just before the the Resonance Cascade to "prepare for unforeseen consequences".[9] To what extent either of these individuals were involved in the authoring of the incident is not at this time known. Adrian Shephard's diary entries also seem to suggest that the event is planned to a degree, as Shephard and the HECU are training and preparing for the mission to Black Mesa a week before the incident even happens.[51]